Cosimo, the cafe's owner, was actually an alien from a temporal inversion fold in the spacetime matrix, who had taken Human form in order to interact with Harry. Cosimo explained to him that history had been changed when Harry's shuttlecraft had intersected with one of his species' timestreams. With Cosimo's help, Harry was able to recreate the accident which created the alternate timeline, and repair the damage to history. (VOY: "Non Sequitur")